具有交替掺入锁核酸（LNA）和2'-（芘-1-基）甲基尿苷的DNA链：单核苷酸多态性（SNP）区分性RNA检测探针。
DNA strands with alternating incorporations of LNA and 2'--(pyren-1-yl)methyluridine: SNP-discriminating RNA detection probes.
作者信息
Karmakar Saswata, Hrdlicka Patrick J
机构信息
University of Idaho, Department of Chemistry, Moscow, ID 83844-2343, USA.
出版信息
Chem Sci. 2013 Sep 1;4(9):3447-3454. doi: 10.1039/C3SC50726B.
Abstract
Detection of nucleic acids using fluorophore-modified oligonucleotides forms the basis of many important applications in molecular biology, genetics and medical diagnostics. Here we demonstrate that DNA strands with central segments of alternating locked nucleic acid (LNA) and 2'--(pyren-1-yl)methyluridine monomers display very large and highly mismatch-sensitive increases in fluorescence emission upon RNA hybridization, whereas corresponding "LNA-free" controls do not. Absorbance spectra strongly suggest that LNA-induced conformational tuning of flanking 2'--(pyren-1-yl)methyluridine monomers places the reporter group in the minor groove upon RNA binding, whereby pyrene-nucleobase interactions leading to quenching of fluorescence are minimized. Accordingly, these easy-to-synthesize probes are promising SNP-discriminating RNA detection probes.
摘要
使用荧光团修饰的寡核苷酸检测核酸是分子生物学、遗传学和医学诊断中许多重要应用的基础。在此我们证明，具有交替的锁核酸（LNA）和2'-（芘-1-基）甲基尿苷单体中心片段的DNA链在与RNA杂交时荧光发射有非常大且高度错配敏感的增加，而相应的“无LNA”对照则没有。吸收光谱强烈表明，LNA诱导的侧翼2'-（芘-1-基）甲基尿苷单体的构象调整使报告基团在与RNA结合时位于小沟中，从而使导致荧光猝灭的芘-核苷酸碱基相互作用最小化。因此，这些易于合成的探针是有前景的单核苷酸多态性（SNP）区分RNA检测探针。
相似文献
1
DNA strands with alternating incorporations of LNA and 2'--(pyren-1-yl)methyluridine: SNP-discriminating RNA detection probes.具有交替掺入锁核酸（LNA）和2'-（芘-1-基）甲基尿苷的DNA链：单核苷酸多态性（SNP）区分性RNA检测探针。
Chem Sci. 2013 Sep 1;4(9):3447-3454. doi: 10.1039/C3SC50726B.
2
Multilabeled pyrene-functionalized 2'-amino-LNA probes for nucleic acid detection in homogeneous fluorescence assays.用于均相荧光分析中核酸检测的多标记芘功能化2'-氨基-LNA探针。
J Am Chem Soc. 2005 Sep 28;127(38):13293-9. doi: 10.1021/ja052887a.
3
High-affinity DNA targeting using readily accessible mimics of N2'-functionalized 2'-amino-α-L-LNA.高亲和力 DNA 靶向使用易于获得的 N2'-功能化 2'-氨基-α-L-LNA 类似物。
J Org Chem. 2011 Sep 2;76(17):7119-31. doi: 10.1021/jo201095p. Epub 2011 Aug 9.
4
Glowing locked nucleic acids: brightly fluorescent probes for detection of nucleic acids in cells.发荧光锁核酸：在细胞中检测核酸的明亮荧光探针。
J Am Chem Soc. 2010 Oct 13;132(40):14221-8. doi: 10.1021/ja1057295.
5
Efficient Discrimination of Single Nucleotide Polymorphisms (SNPs) Using Oligonucleotides Modified with C5-Pyrene-Functionalized DNA and Flanking Locked Nucleic Acid (LNA) Monomers.使用经C5-芘功能化DNA和侧翼锁核酸（LNA）单体修饰的寡核苷酸高效鉴别单核苷酸多态性（SNP）
Chem Asian J. 2016 May 6;11(9):1366-9. doi: 10.1002/asia.201600200. Epub 2016 Apr 5.
6
Locked nucleic acid (LNA) induced effect on the hybridization and fluorescence properties of oligodeoxyribonucleotides modified with nucleobase-functionalized DNA monomers.锁核酸（LNA）对用碱基功能化DNA单体修饰的寡脱氧核糖核苷酸的杂交和荧光性质的诱导作用。
Org Biomol Chem. 2015 Jul 14;13(26):7236-47. doi: 10.1039/c5ob00860c. Epub 2015 Jun 9.
7
C5-functionalized DNA, LNA, and α-L-LNA: positional control of polarity-sensitive fluorophores leads to improved SNP-typing.C5- 功能化 DNA、锁核酸和 α-L-锁核酸：极性敏感荧光团的位置控制导致 SNP 分型的改善。
Chemistry. 2011 Mar 7;17(11):3157-65. doi: 10.1002/chem.201002109. Epub 2011 Feb 15.
8
Synthesis and characterization of oligodeoxyribonucleotides modified with 2'-thio-2'-deoxy-2'-S-(pyren-1-yl)methyluridine.用2'-硫代-2'-脱氧-2'-S-(芘-1-基)甲基尿苷修饰的寡脱氧核糖核苷酸的合成与表征
Bioorg Med Chem Lett. 2015 Sep 15;25(18):3999-4004. doi: 10.1016/j.bmcl.2015.07.002. Epub 2015 Jul 7.
9
Unlocked nucleic acids with a pyrene-modified uracil: synthesis, hybridization studies, fluorescent properties and i-motif stability.带有芘修饰尿嘧啶的非锁核酸：合成、杂交研究、荧光性质和 i 型发夹结构稳定性。
Chembiochem. 2014 Jan 3;15(1):146-56. doi: 10.1002/cbic.201300567.
10
Identification and characterization of second-generation invader locked nucleic acids (LNAs) for mixed-sequence recognition of double-stranded DNA.鉴定和表征第二代入侵锁核酸（LNA），用于双链 DNA 的混合序列识别。
J Org Chem. 2013 Oct 4;78(19):9560-70. doi: 10.1021/jo4015936. Epub 2013 Sep 25.
引用本文的文献
1
SPEAR: CRISPR-mediated ultrasensitive, specific and rapid one-pot detection strategy for cancer-related SNPs.SPEAR：用于癌症相关单核苷酸多态性的CRISPR介导的超灵敏、特异且快速的一锅法检测策略。
Theranostics. 2025 Feb 18;15(8):3275-3288. doi: 10.7150/thno.107488. eCollection 2025.
2
Universal and high-fidelity DNA single nucleotide polymorphism detection based on a CRISPR/Cas12a biochip.基于CRISPR/Cas12a生物芯片的通用且高保真的DNA单核苷酸多态性检测
Chem Sci. 2021 Feb 9;12(12):4455-4462. doi: 10.1039/d0sc05717g.
3
Intracellular fluorometric determination of microRNA-21 by using a switch-on nanoprobe composed of carbon nanotubes and gold nanoclusters.利用由碳纳米管和金纳米簇组成的开关型纳米探针细胞内荧光测定 microRNA-21
Mikrochim Acta. 2019 Jun 13;186(7):447. doi: 10.1007/s00604-019-3573-8.
4
A multiplex one-tube nested real time RT-PCR assay for simultaneous detection of respiratory syncytial virus, human rhinovirus and human metapneumovirus.一种用于同时检测呼吸道合胞病毒、人类鼻病毒和人类偏肺病毒的多重单管巢式实时 RT-PCR 检测方法。
Virol J. 2018 Oct 30;15(1):167. doi: 10.1186/s12985-018-1061-0.
5
A highly sensitive 1-tube nested real-time RT-PCR assay using LNA-modified primers for detection of respiratory syncytial virus.一种使用锁核酸（LNA）修饰引物的高灵敏度单管巢式实时逆转录聚合酶链反应（RT-PCR）检测方法，用于检测呼吸道合胞病毒。
Diagn Microbiol Infect Dis. 2019 Feb;93(2):101-106. doi: 10.1016/j.diagmicrobio.2018.09.001. Epub 2018 Sep 8.
6
In vitro inhibition of porcine reproductive and respiratory syndrome virus replication by short antisense oligonucleotides with locked nucleic acid modification.具有锁核酸修饰的短反义寡核苷酸对猪繁殖与呼吸综合征病毒复制的体外抑制作用
BMC Vet Res. 2018 Mar 26;14(1):109. doi: 10.1186/s12917-018-1432-1.
7
Recent Advances in Nucleic Acid Targeting Probes and Supramolecular Constructs Based on Pyrene-Modified Oligonucleotides.基于芘修饰寡核苷酸的核酸靶向探针和超分子构建的最新进展。
Molecules. 2017 Nov 30;22(12):2108. doi: 10.3390/molecules22122108.
8
25 years and still going strong: 2'-O-(pyren-1-yl)methylribonucleotides - versatile building blocks for applications in molecular biology, diagnostics and materials science.25年依然强劲：2'-O-（芘-1-基）甲基核糖核苷酸——分子生物学、诊断学和材料科学应用中的多功能构建模块。
Org Biomol Chem. 2017 Nov 29;15(46):9760-9774. doi: 10.1039/c7ob02152f.
9
Synthesis and characterization of oligodeoxyribonucleotides modified with 2'-thio-2'-deoxy-2'-S-(pyren-1-yl)methyluridine.用2'-硫代-2'-脱氧-2'-S-(芘-1-基)甲基尿苷修饰的寡脱氧核糖核苷酸的合成与表征
Bioorg Med Chem Lett. 2015 Sep 15;25(18):3999-4004. doi: 10.1016/j.bmcl.2015.07.002. Epub 2015 Jul 7.
10
Protected DNA strand displacement for enhanced single nucleotide discrimination in double-stranded DNA.用于增强双链DNA中单个核苷酸识别的保护性DNA链置换
Sci Rep. 2015 Mar 4;5:8721. doi: 10.1038/srep08721.
本文引用的文献
1
Large scale synthesis of 2'-amino-LNA thymine and 5-methylcytosine nucleosides.2'-氨基-LNA 胸腺嘧啶和 5-甲基胞嘧啶核苷的大规模合成。
J Org Chem. 2012 Dec 7;77(23):10718-28. doi: 10.1021/jo302036h. Epub 2012 Nov 26.
2
Imaging of RNA in live cells.活细胞内 RNA 的成像。
Curr Opin Chem Biol. 2011 Dec;15(6):806-12. doi: 10.1016/j.cbpa.2011.10.006. Epub 2011 Nov 4.
3
An overview of sugar-modified oligonucleotides for antisense therapeutics.用于反义治疗的糖修饰寡核苷酸概述。
Chem Biodivers. 2011 Sep;8(9):1616-41. doi: 10.1002/cbdv.201100081.
4
High-affinity DNA targeting using readily accessible mimics of N2'-functionalized 2'-amino-α-L-LNA.高亲和力 DNA 靶向使用易于获得的 N2'-功能化 2'-氨基-α-L-LNA 类似物。
J Org Chem. 2011 Sep 2;76(17):7119-31. doi: 10.1021/jo201095p. Epub 2011 Aug 9.
5
Pyrene-functionalized oligonucleotides and locked nucleic acids (LNAs): tools for fundamental research, diagnostics, and nanotechnology.芘基化寡核苷酸和锁核酸 (LNA)：基础研究、诊断和纳米技术的工具。
Chem Soc Rev. 2011 Dec;40(12):5771-88. doi: 10.1039/c1cs15014f. Epub 2011 Apr 13.
6
LNA for optimization of fluorescent oligonucleotide probes: improved spectral properties and target binding.寡核苷酸荧光探针的优化用 LNAs：改善光谱性质和靶标结合。
Bioconjug Chem. 2011 Apr 20;22(4):533-9. doi: 10.1021/bc1005027. Epub 2011 Mar 14.
7
C5-functionalized DNA, LNA, and α-L-LNA: positional control of polarity-sensitive fluorophores leads to improved SNP-typing.C5- 功能化 DNA、锁核酸和 α-L-锁核酸：极性敏感荧光团的位置控制导致 SNP 分型的改善。
Chemistry. 2011 Mar 7;17(11):3157-65. doi: 10.1002/chem.201002109. Epub 2011 Feb 15.
8
Novel insights into the use of Glowing LNA as nucleic acid detection probes--influence of labeling density and nucleobases.关于利用发光 LNA 作为核酸检测探针的新见解——标记密度和碱基的影响。
Bioorg Med Chem Lett. 2010 Dec 15;20(24):7265-8. doi: 10.1016/j.bmcl.2010.10.089. Epub 2010 Nov 9.
9
Nucleic acid-based fluorescent probes and their analytical potential.基于核酸的荧光探针及其分析潜力。
Anal Bioanal Chem. 2011 Mar;399(9):3157-76. doi: 10.1007/s00216-010-4304-5. Epub 2010 Oct 29.
10
Novel interstrand communication systems within DNA duplexes based on 1-, 2- and 4-(phenylethynyl)pyrenes attached to 2'-amino-LNA: high-affinity hybridization and fluorescence sensing.基于连接到 2'-氨基-LNA 的 1-、2- 和 4-（苯乙炔基）芘的 DNA 双链体中的新型链间通信系统：高亲和力杂交和荧光传感。
Chem Commun (Camb). 2010 Nov 28;46(44):8362-4. doi: 10.1039/c0cc03026k. Epub 2010 Oct 4.
Zotero 插件